Browse Articles

  • Article |

    It remains impossible using conventional Hi-C to differentiate interactions between and along sister chromatids. SisterC relies on selective destruction of nascent DNA and in combination with Hi-C offers a means to study intra- and inter-sister interactions independently.

    • Marlies E. Oomen
    • , Adam K. Hedger
    • , Jonathan K. Watts
    •  & Job Dekker
  • Article |

    Plasmonic scattering microscopy (PSM) enables the imaging of single proteins on SPR instruments. The method enables measurement of protein size and binding kinetics and is fully compatible with simultaneous traditional SPR measurements.

    • Pengfei Zhang
    • , Guangzhong Ma
    • , Wei Dong
    • , Zijian Wan
    • , Shaopeng Wang
    •  & Nongjian Tao
  • Brief Communication |

    MassIVE.quant is a data repository and data resource for reproducible quantitative mass spectrometry–based proteomics.

    • Meena Choi
    • , Jeremy Carver
    • , Cristina Chiva
    • , Manuel Tzouros
    • , Ting Huang
    • , Tsung-Heng Tsai
    • , Benjamin Pullman
    • , Oliver M. Bernhardt
    • , Ruth Hüttenhain
    • , Guo Ci Teo
    • , Yasset Perez-Riverol
    • , Jan Muntel
    • , Maik Müller
    • , Sandra Goetze
    • , Maria Pavlou
    • , Erik Verschueren
    • , Bernd Wollscheid
    • , Alexey I. Nesvizhskii
    • , Lukas Reiter
    • , Tom Dunkley
    • , Eduard Sabidó
    • , Nuno Bandeira
    •  & Olga Vitek
  • Article |

    Tension-PAINT integrates molecular tension probes with DNA-PAINT to enable ~25-nm-resolution mapping of piconewton mechanical events. Tension-PAINT can be used to study dynamic forces, and an irreversible variant integrates force history over time.

    • Joshua M. Brockman
    • , Hanquan Su
    • , Aaron T. Blanchard
    • , Yuxin Duan
    • , Travis Meyer
    • , M. Edward Quach
    • , Roxanne Glazier
    • , Alisina Bazrafshan
    • , Rachel L. Bender
    • , Anna V. Kellner
    • , Hiroaki Ogasawara
    • , Rong Ma
    • , Florian Schueder
    • , Brian G. Petrich
    • , Ralf Jungmann
    • , Renhao Li
    • , Alexa L. Mattheyses
    • , Yonggang Ke
    •  & Khalid Salaita
  • Article |

    Antigen-specific CD8+ T cells can be imaged by immunoPET with the help of synTacs, MHC-based tools that bind to relevant T-cell receptors.

    • Andrew W. Woodham
    • , Stad H. Zeigler
    • , Ella L. Zeyang
    • , Stephen C. Kolifrath
    • , Ross W. Cheloha
    • , Mohammad Rashidian
    • , Rodolfo J. Chaparro
    • , Ronald D. Seidel
    • , Scott J. Garforth
    • , Jason L. Dearling
    • , Maia Mesyngier
    • , Phaneendra K. Duddempudi
    • , Alan B. Packard
    • , Steven C. Almo
    •  & Hidde L. Ploegh
  • This Month |

    Frugally built technology to study the ocean’s microbes, and engineering for societal good.

    • Vivien Marx
  • Article |

    Temporal decomposition through manifold fitting (TDM) is an analysis technique that decomposes blood oxygenation level dependent (BOLD) responses in task-based fMRI into different components that likely correspond to microvasculature- and macrovasculature-driven signals.

    • Kendrick Kay
    • , Keith W. Jamison
    • , Ru-Yuan Zhang
    •  & Kamil Uğurbil
  • Article |

    Red and yellow versions of the genetically encoded dopamine sensor dLight1 have been developed and allow multiplexed imaging of dopamine with neurotransmitter or cell-type-specific calcium combined with green sensors or actuators, as demonstrated ex vivo and in behaving rodents.

    • Tommaso Patriarchi
    • , Ali Mohebi
    • , Junqing Sun
    • , Aaron Marley
    • , Ruqiang Liang
    • , Chunyang Dong
    • , Kyle Puhger
    • , Grace Or Mizuno
    • , Carolyn M. Davis
    • , Brian Wiltgen
    • , Mark von Zastrow
    • , Joshua D. Berke
    •  & Lin Tian
  • Research Highlight |

    Addition of a second constriction to CsgG-family nanopores improves the accuracy of homopolymer sequencing.

    • Arunima Singh
  • Editorial |

    We distributed an informal questionnaire to learn from scientists about their professional use of WeChat. We share some of their answers and discuss the multipurpose platform offered by WeChat.

  • Research Highlight |

    BRICseq provides access to brain-wide connectivity and can be combined with functional and transcriptomic studies for a comprehensive view of neuronal circuitry.

    • Nina Vogt
  • Article |

    ScNT-seq leverages metabolic labeling of nascent RNA and droplet-based sequencing for parallel analysis of newly transcribed and pre-existing mRNAs, which enables time-resolved analysis of dynamic biological processes in single cells.

    • Qi Qiu
    • , Peng Hu
    • , Xiaojie Qiu
    • , Kiya W. Govek
    • , Pablo G. Cámara
    •  & Hao Wu
  • This Month |

    “I have no idea what’s awaiting me, or what will happen when this all ends. For the moment I know this: there are sick people and they need curing.” ―Albert Camus, The Plague

    • Katriona Shea
    • , Ottar N. Bjørnstad
    • , Martin Krzywinski
    •  & Naomi Altman
  • Brief Communication |

    Feature-based molecular networking allows the generation of molecular networks for mass spectrometry data that can recognize isomers, incorporate relative quantification and integrate ion mobility data.

    • Louis-Félix Nothias
    • , Daniel Petras
    • , Robin Schmid
    • , Kai Dührkop
    • , Johannes Rainer
    • , Abinesh Sarvepalli
    • , Ivan Protsyuk
    • , Madeleine Ernst
    • , Hiroshi Tsugawa
    • , Markus Fleischauer
    • , Fabian Aicheler
    • , Alexander A. Aksenov
    • , Oliver Alka
    • , Pierre-Marie Allard
    • , Aiko Barsch
    • , Xavier Cachet
    • , Andres Mauricio Caraballo-Rodriguez
    • , Ricardo R. Da Silva
    • , Tam Dang
    • , Neha Garg
    • , Julia M. Gauglitz
    • , Alexey Gurevich
    • , Giorgis Isaac
    • , Alan K. Jarmusch
    • , Zdeněk Kameník
    • , Kyo Bin Kang
    • , Nikolas Kessler
    • , Irina Koester
    • , Ansgar Korf
    • , Audrey Le Gouellec
    • , Marcus Ludwig
    • , Christian Martin H.
    • , Laura-Isobel McCall
    • , Jonathan McSayles
    • , Sven W. Meyer
    • , Hosein Mohimani
    • , Mustafa Morsy
    • , Oriane Moyne
    • , Steffen Neumann
    • , Heiko Neuweger
    • , Ngoc Hung Nguyen
    • , Melissa Nothias-Esposito
    • , Julien Paolini
    • , Vanessa V. Phelan
    • , Tomáš Pluskal
    • , Robert A. Quinn
    • , Simon Rogers
    • , Bindesh Shrestha
    • , Anupriya Tripathi
    • , Justin J. J. van der Hooft
    • , Fernando Vargas
    • , Kelly C. Weldon
    • , Michael Witting
    • , Heejung Yang
    • , Zheng Zhang
    • , Florian Zubeil
    • , Oliver Kohlbacher
    • , Sebastian Böcker
    • , Theodore Alexandrov
    • , Nuno Bandeira
    • , Mingxun Wang
    •  & Pieter C. Dorrestein
  • Technology Feature |

    With advanced approaches to sample preparation and data analysis, scientists doing cryo-EM are starting to infer molecular movements from samples that are, literally, frozen.

    • Amber Dance
  • This Month |

    A new way to see actin in action, hearing as others don’t, and saved by the guitar.

    • Vivien Marx
  • News & Views |

    Plankton regularly travel vast distances up and down in the ocean. A water-filled hamster wheel with glass windows now enables detailed microscopic lab observations of individual aquatic microorganisms during their vertical migrations.

    • Katja M. Taute
  • Article |

    Scale-free vertical tracking microscopy based on a ‘hydrodynamic treadmill’ enables measuring long-range movements of freely suspended organisms with high spatiotemporal resolution.

    • Deepak Krishnamurthy
    • , Hongquan Li
    • , François Benoit du Rey
    • , Pierre Cambournac
    • , Adam G. Larson
    • , Ethan Li
    •  & Manu Prakash
  • Brief Communication |

    Repository-scale reanalysis of public mass spectrometry-based metabolomics data is facilitated by the Reanalysis of Data User (ReDU) interface, a system that uses consistent formatting and controlled vocabularies for metadata capture.

    • Alan K. Jarmusch
    • , Mingxun Wang
    • , Christine M. Aceves
    • , Rohit S. Advani
    • , Shaden Aguirre
    • , Alexander A. Aksenov
    • , Gajender Aleti
    • , Allegra T. Aron
    • , Anelize Bauermeister
    • , Sanjana Bolleddu
    • , Amina Bouslimani
    • , Andres Mauricio Caraballo Rodriguez
    • , Rama Chaar
    • , Roxana Coras
    • , Emmanuel O. Elijah
    • , Madeleine Ernst
    • , Julia M. Gauglitz
    • , Emily C. Gentry
    • , Makhai Husband
    • , Scott A. Jarmusch
    • , Kenneth L. Jones II
    • , Zdenek Kamenik
    • , Audrey Le Gouellec
    • , Aileen Lu
    • , Laura-Isobel McCall
    • , Kerry L. McPhail
    • , Michael J. Meehan
    • , Alexey V. Melnik
    • , Riya C. Menezes
    • , Yessica Alejandra Montoya Giraldo
    • , Ngoc Hung Nguyen
    • , Louis Felix Nothias
    • , Mélissa Nothias-Esposito
    • , Morgan Panitchpakdi
    • , Daniel Petras
    • , Robert A. Quinn
    • , Nicole Sikora
    • , Justin J. J. van der Hooft
    • , Fernando Vargas
    • , Alison Vrbanac
    • , Kelly C. Weldon
    • , Rob Knight
    • , Nuno Bandeira
    •  & Pieter C. Dorrestein
  • Article |

    A method based on maximum likelihood density modification, adapted from X-ray crystallography, improves cryo-EM maps.

    • Thomas C. Terwilliger
    • , Steven J. Ludtke
    • , Randy J. Read
    • , Paul D. Adams
    •  & Pavel V. Afonine
  • Brief Communication |

    A spraying-mixing approach for preparing cryo-EM grids using the Spotiton robot allows time-resolved observations of short-lived biomolecular states.

    • Venkata P. Dandey
    • , William C. Budell
    • , Hui Wei
    • , Daija Bobe
    • , Kashyap Maruthi
    • , Mykhailo Kopylov
    • , Edward T. Eng
    • , Peter A. Kahn
    • , Jenny E. Hinshaw
    • , Nidhi Kundu
    • , Crina M. Nimigean
    • , Chen Fan
    • , Nattakan Sukomon
    • , Seth A. Darst
    • , Ruth M. Saecker
    • , James Chen
    • , Brandon Malone
    • , Clinton S. Potter
    •  & Bridget Carragher
  • Brief Communication |

    Genetically encoded fluorescent-protein-tagged actin nanobodies fused to organelle membrane-targeting sequences enables high-resolution imaging of transient organelle–actin contact sites in live cells.

    • Cara R. Schiavon
    • , Tong Zhang
    • , Bing Zhao
    • , Andrew S. Moore
    • , Pauline Wales
    • , Leonardo R. Andrade
    • , Melissa Wu
    • , Tsung-Chang Sung
    • , Yelena Dayn
    • , Jasmine W. Feng
    • , Omar A. Quintero
    • , Gerald S. Shadel
    • , Robert Grosse
    •  & Uri Manor
  • Article |

    Genetically encoded cysteine-rich tags enable formation of gold nanoparticles in situ for single-molecule imaging of individual proteins in the context of cellular ultrastructure in bacterial, yeast and mammalian cells.

    • Zhaodi Jiang
    • , Xiumei Jin
    • , Yuhua Li
    • , Sitong Liu
    • , Xiao-Man Liu
    • , Ying-Ying Wang
    • , Pei Zhao
    • , Xinbin Cai
    • , Ying Liu
    • , Yaqi Tang
    • , Xiaobin Sun
    • , Yan Liu
    • , Yanyong Hu
    • , Ming Li
    • , Gaihong Cai
    • , Xiangbing Qi
    • , She Chen
    • , Li-Lin Du
    •  & Wanzhong He
  • Author Correction
    | Open Access

    • Wei Ouyang
    • , Casper F. Winsnes
    • , Martin Hjelmare
    • , Anthony J. Cesnik
    • , Lovisa Åkesson
    • , Hao Xu
    • , Devin P. Sullivan
    • , Shubin Dai
    • , Jun Lan
    • , Park Jinmo
    • , Shaikat M. Galib
    • , Christof Henkel
    • , Kevin Hwang
    • , Dmytro Poplavskiy
    • , Bojan Tunguz
    • , Russel D. Wolfinger
    • , Yinzheng Gu
    • , Chuanpeng Li
    • , Jinbin Xie
    • , Dmitry Buslov
    • , Sergei Fironov
    • , Alexander Kiselev
    • , Dmytro Panchenko
    • , Xuan Cao
    • , Runmin Wei
    • , Yuanhao Wu
    • , Xun Zhu
    • , Kuan-Lun Tseng
    • , Zhifeng Gao
    • , Cheng Ju
    • , Xiaohan Yi
    • , Hongdong Zheng
    • , Constantin Kappel
    •  & Emma Lundberg
  • Article |

    Chemically inducible trimerization tools based on split FRB or FKBP with full-length FKBP or FRB, respectively, expand the chemogenetics toolbox. Their efficiency and fast kinetics enable new types of protein manipulation in live cells.

    • Helen D. Wu
    • , Masaki Kikuchi
    • , Onur Dagliyan
    • , Adam K. Aragaki
    • , Hideki Nakamura
    • , Nikolay V. Dokholyan
    • , Takashi Umehara
    •  & Takanari Inoue
  • Research Highlight |

    Tethering fluorescent proteins to ribosomes clears up background signals when imaging neural circuits.

    • Nina Vogt
  • Research Highlight |

    Intravital three-dimensional bioprinting enables the biofabrication of constructs in a pre-existing 3D matrix, such as inside tissues of live animals.

    • Lei Tang
  • Research Highlight |

    RIC-seq enables in situ mapping of intra- and intermolecular RNA–RNA interactions.

    • Lin Tang
  • Research Highlight |

    barRNAseq allows detailed explorations of signaling pathways that control embryonic differentiation.

    • Madhura Mukhopadhyay
  • Research Highlight |

    Direct imaging of carbohydrates using electrospray ion beam deposition and scanning tunneling microscopy.

    • Arunima Singh
  • Editorial |

    We’ve made some recent updates to our various content type offerings at Nature Methods. Here is a cheat sheet.

  • Article |

    Supervised machine-learning models trained using Drosophila epigenetic and STARR-seq data can be transferred to predict mouse and human enhancers.

    • Anurag Sethi
    • , Mengting Gu
    • , Emrah Gumusgoz
    • , Landon Chan
    • , Koon-Kiu Yan
    • , Joel Rozowsky
    • , Iros Barozzi
    • , Veena Afzal
    • , Jennifer A. Akiyama
    • , Ingrid Plajzer-Frick
    • , Chengfei Yan
    • , Catherine S. Novak
    • , Momoe Kato
    • , Tyler H. Garvin
    • , Quan Pham
    • , Anne Harrington
    • , Brandon J. Mannion
    • , Elizabeth A. Lee
    • , Yoko Fukuda-Yuzawa
    • , Axel Visel
    • , Diane E. Dickel
    • , Kevin Y. Yip
    • , Richard Sutton
    • , Len A. Pennacchio
    •  & Mark Gerstein
  • Article |

    A general tuning strategy is introduced for improving the utility of rhodamines for biological imaging applications. The strategy yielded bright, versatile and bioavailable far-red and near-infrared ‘Janelia Fluor’ dyes.

    • Jonathan B. Grimm
    • , Ariana N. Tkachuk
    • , Liangqi Xie
    • , Heejun Choi
    • , Boaz Mohar
    • , Natalie Falco
    • , Kathy Schaefer
    • , Ronak Patel
    • , Qinsi Zheng
    • , Zhe Liu
    • , Jennifer Lippincott-Schwartz
    • , Timothy A. Brown
    •  & Luke D. Lavis